It starts at the confluence of the rivers Chaguane and Huinchuta and flows for 54 kilometres (34 mi) before reaching the Laguna Mucalliri of the Salar de Coipasa.

[3] The Chaguane is 12 kilometres (7.5 mi) long and receives water from the Laguna Parinacota,[4] which in turn is nourished from two creeks that join it from the west and north.

[2] After the confluence, the Isluga River proceeds in southeast-eastward direction save for a brief turn northeast, past the towns of Chaguane and Arabilla; between the two the Quebrada Taipicollo joins from the northwest.

After this turn the river continues first southeast-east, then due east between Cachaguano and Isluga where it has a slight northeasterly tilt, and finally southeastward towards Sitani and Cotasaya.

[2] After a total course of 54 kilometres (34 mi) before ending into the Laguna Mucalliri, which is part of a system of wetlands at Salar de Coipasa.

From the south it receives tributaries from the Sierra Uscana,[7] including the 54 kilometres (34 mi) long Mauque which joins the Isluga River in the Fisica Choque/Chaque wetland.

The salinity is dominated by chloride, sodium and sulfate[17] owing to high evaporation and the dissolution of salts in the catchment.

[25] The Peru water frog has also been found,[27] as are several mollusc species of the taxa chilinidae and veneroida[28] and snails of the genus Heleobia.

[29] A number of different plant species grow in the waters of the Isluga River,[30] such as Carex, Catabrosa verdermanni, Deschampsia caespitosa, Deyeuxia curvula, Drabella, Distichia muscoides, Distichlis humilis, Eleocharis, Festuca nardifolia, Juncus, Lilaeopsis lineata, Oxychloe andina, Potamogeton strictum, Ranunculus, Sarcocornia pulvinata, Scirpus atacamensis and Triglochin palustris.

[31] The steppes surrounding the catchment feature a flora which includes quenoa and yareta; depending on the availability of water different places are dominated by different plants.

[32] Among the fauna are flamingos and vicuñas, lizards of the genus Liolaemus, the frog Pleurodema marmoratum and the toad Rhinella spinulosa.